Blog post: Highlighting RO-Crate Features in Galaxy

docs/_blog/.template.md

@@ -49,10 +49,10 @@ _blog/
  You can then include the image in the Markdown text with the following code:
 
 ```
-{% include image.html src="my_image.png" caption="A test image" alt="Description of image" %}
+{% include image.html src="my_image.png" caption="A test image" alt="Description of image" border=false %}
 ```
 
-Set `src` to the image path, then set `caption` and `alt` to appropriate descriptions of the image. The `caption` will be displayed on the page, while the `alt` will be used for the image alternative description (used by screen readers).
+Set `src` to the image path, then set `caption` and `alt` to appropriate descriptions of the image. The `caption` will be displayed on the page, while the `alt` will be used for the image alternative description (used by screen readers). Set `border` to `true` to show a border around the image - this is useful for ensuring screenshots containing a lot of whitespace are properly distinguished from the rest of the text.
 
 ## Including internal links
 

docs/_blog/2026-01-14/highlighting-ro-crate-features-in-galaxy.md

@@ -0,0 +1,64 @@
+---
+title:  "Highlighting RO-Crate Features in Galaxy"
+author: ["Eli Chadwick"]
+date: 2026-01-14
+related_pages:
+    use_cases: [galaxy, workflowhub, eln] # should match items in pages/use_cases
+---
+
+[Galaxy](https://galaxyproject.org) is an open-source platform for FAIR data analysis. It enables users to create and run their own workflows, and includes tools from a wide range of scientific domains. 
+
+RO-Crate and WorkflowHub support was integrated into Galaxy as part of the [EuroScienceGateway](https://galaxyproject.org/projects/esg/) project which ran from September 2022 to August 2025.
+
+The RO-Crate integration is designed to be usable by anyone, including users who do not know what RO-Crate is. Galaxy populates the RO-Crate metadata automatically using information it has stored - including metadata that users have added themselves through the Galaxy interface when completing tasks like creating a workflow. Users do not need to worry about the technicalities of the format, they simply benefit from it by default when importing/exporting data.
+
+## Importing data as RO-Crate
+
+Galaxy has a [ZIP explorer integration](https://docs.galaxyproject.org/en/master/releases/25.0_announce_user.html#add-zip-explorer-to-import-individual-files-from-local-or-remote-zip-archives) which allows the user to import individual files from ZIP archives. When importing [a ZIP file that is also an RO-Crate]({{baseurl}}{% link _specification/1.2/structure.md %}#attached-ro-crate-package), core metadata is extracted from the RO-Crate and displayed when exploring the ZIP.
+
+{% include image.html src="galaxy-import-ro-crate.png" caption="Galaxy ZIP explorer showing metadata extracted from RO-Crate." alt="Galaxy ZIP explorer showing dataset title, publication date, DOI, description, license, creators, institutions, and RO-Crate profiles." %}
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/oqEUHoCcEPo?si=bwR3KekmBjw_LCsR" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+## Exporting data as RO-Crate
+
+A Galaxy history can be exported to a file, which can be downloaded directly or [uploaded to data repositories](https://galaxyproject.org/news/2025-03-10-inveniordm-integration-update/) like Zenodo. The default format for an exported history is an RO-Crate ZIP file.
+
+{% include image.html src="galaxy-export-history.png" caption="Galaxy history export to Zenodo sandbox." alt="Galaxy history export view configured to publish to Zenodo with the file name 'My test history'" border=true %}
+
+{% include image.html src="zenodo-exported-ro-crate.png" caption="Draft Zenodo record with Galaxy history uploaded as RO-Crate." alt="Zenodo draft record showing a file called 'My test history.rocrate.zip'" border=true %}
+
+## Exporting workflow invocation as RO-Crate
+
+An individual invocation of a Galaxy workflow can be [exported as a RO-Crate](https://galaxyproject.org/news/2023-02-23-structured-data-exports-ro-bco/) following the [Workflow Run Crate](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/) profile. As with the history export, the output can be downloaded as a file or uploaded to a data repository. The workflow file, inputs, outputs, and Galaxy metadata are included in the RO-Crate.
+
+{% include image.html src="galaxy-export-workflow-invocation.png" caption="Export a workflow invocation from Galaxy in formats including Workflow Run RO-Crate." alt="Galaxy workflow invocation export page with Workflow Run RO-Crate selected as the output format" border=true %}
+
+## Re-import exported RO-Crates!
+
+Because Galaxy can import RO-Crates, you can re-import an exported workflow invocation or history back into Galaxy. This facilitates reproducibility of workflow runs, as well as general reuse of exported data (for example, you could import just the workflow file from an invocation and then run that workflow with different data).
+
+{% include image.html src="galaxy-reimport-exported-ro-crate.png" caption="Reimporting a Workflow Run RO-Crate exported from Galaxy." alt="Galaxy ZIP explorer showing RO-Crate metadata from the workflow invocation which was exported earlier. It is tagged with 'Galaxy Workflow Run' as well as 'RO-Crate' in the interface. The metadata says it was automatically generated by Galaxy and includes both the timestamp of the invocation and the timestamp of publication." border=true %}
+
+## WorkflowHub integration
+
+Galaxy is also closely integrated with the WorkflowHub workflow registry. Any workflow registered on WorkflowHub can be exported from WorkflowHub as a Workflow RO-Crate.
+
+In the Galaxy interface, you can [import workflows from WorkflowHub](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_run_wfh.html). In the WorkflowHub interface, Galaxy workflows are shown with a button to launch the workflow in a Galaxy instance where the required tools are available.
+
+Workflows developed by the Intergalactic Workflow Commission and the Galaxy Training Network are [automatically registered with WorkflowHub](https://training.galaxyproject.org/training-material/news/2025/09/02/gtn-workflowhub.html), enhancing their FAIRness.
+
+{% include image.html src="wfh-galaxy-integration.png" caption="Galaxy supports import from WorkflowHub, and WorkflowHub workflows can be directly launched in Galaxy." alt="On the left, the Galaxy workflow import page showing workflowhub.eu circled as the TRS Server source. On the right, a workflow page on WorkflowHub with the 'Run in Galaxy' button circled."%}
+
+
+## ELN integration
+
+Galaxy can already integrate with [RSpace](https://www.researchspace.com) and [eLabFTW](https://www.elabftw.net), which are [Electronic Lab Notebook (ELN)]({{baseurl}}{% link pages/use_cases/eln.md %}) platforms. Both of these platforms are part of the [ELN consortium](https://the.elnconsortium.org), a community which develops standards for interoperable ELNs, including the [ELN file format](https://github.com/TheELNConsortium/TheELNFileFormat) which is based on RO-Crate.
+
+RO-Crate therefore offers opportunities for even closer integration and interoperability between Galaxy and ELNs in the future.
+
+## Training Material
+
+The [Galaxy Training Network](https://training.galaxyproject.org) includes a collection of tutorials on [making workflows FAIR with RO-Crate](https://training.galaxyproject.org/training-material/topics/fair/#st-ro-crate). This includes tutorials on exporting Workflow Run RO-Crates from Galaxy as seen above, and adding tests to a Galaxy workflow to create a [Workflow Testing RO-Crate](https://lifemonitor.eu/workflow_testing_ro_crate). Development of these tutorials was supported by the [BY-COVID](https://by-covid.org) project.
+
+There are also tutorials on domain-specific RO-Crate applications: [DataPLANT ARCs](https://training.galaxyproject.org/training-material/topics/fair/#st-dataplant) (from the [DataPLANT](https://nfdi4plants.org/) project) and [An earth system RO-Crate](https://training.galaxyproject.org/training-material/topics/fair/#st-other) (from the [FAIR-EASE](https://fairease.eu) project).

docs/_includes/image.html

@@ -1,4 +1,8 @@
 <figure class="image">
-  <img src="{{ include.src }}" alt="{{ include.alt }}" style="max-width:90%">
+  <img src="{{ include.src }}" alt="{{ include.alt }}" style="max-width:90%" 
+  {% if include.border %}
+  class="border border-dark"
+  {% endif %}
+  >
   <figcaption>{{ include.caption }}</figcaption>
 </figure>

docs/pages/use_cases/eln.md

@@ -1,7 +1,7 @@
 ---
 page_id: eln
 title: Electronic Lab Notebook
-description: 
+description: The ELN file format has been defined as an archive format to capture Electronic Laboratory Notebooks (ELN). The format is based on RO-Crate and is supported by a number of ELN softwares.
 url: https://guides.dataverse.org/en/6.4/installation/advanced.html#inventory-of-external-exporters
 domains: [chemistry, biomedical_science]
 tasks: [data_handling, manage_data]